Jacobsen was born on July 16, 1982, on Long Island outside New York City. His father, Edmund Jacobsen, was a violinist and one-time member of the Metropolitan Opera Orchestra; his mother, Ivy Jacobsen, was a flutist. Jacobsen and his brother Colin were exposed to classical music at musicales in the family home. Jacobsen attended the Juilliard School in Manhattan, where he studied with Harvey Shapiro and Joseph Elworthy. The two Jacobsen brothers co-founded the Brooklyn Rider string quartet in 2004; the group, with Eric on cello, has specialized in high-energy, accessible performances of contemporary music and has won attention for appearances not only at such traditional venues as Carnegie Hall and Lincoln Center in New York but also for concerts at the South by Southwest festival and the San Francisco Jazz Festival. The New York orchestra The Knights also grew from a collaboration between the two Jacobsen brothers, who as students in the late 1990s, gathered friends to explore chamber orchestra repertory; these ad hoc meetings grew into a permanent institution that has collaborated with artists of the stature of Ma, soprano Dawn Upshaw, and violinist Itzhak Perlman. Eric has conducted the group at concerts in both the U.S. and Europe, including at the Dresden Musikfestpiele in Germany. In the fall of 2014, Jacobsen began appointments as the principal conductor of Connecticut's Greater Bridgeport Symphony and as an artistic partner at the Northwest Sinfonietta in Washington state. A year later, he began a five-year term as the music director of the Orlando Philharmonic. Jacobsen is married to folk singer-songwriter Aoife O'Donovan.
Jacobsen's recording career began in 2006 when he played cello on the soundtrack of the film The Departed, and he has appeared on several other film soundtracks. The following year, he appeared on the Silkroad Ensemble album New Impossibilities, and he has recorded with all three of the major ensembles with which he has been associated, often conducting The Knights. Jacobsen has played cello on albums by artists from beyond the classical sphere, including O'Donovan and songwriter Suzanne Vega. In 2021, he conducted The Knights on a recording by violinist Gil Shaham of the Beethoven and Brahms violin concertos on the Canary Classics label. ~ James Manheim, Rovi